Variant report

Variant	rs10880874
Chromosome Location	chr12:46359832-46359833
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46359781..46361331-chr12:46365330..46366912,2	K562	blood:
2	chr12:46354837..46356506-chr12:46359246..46361993,2	MCF-7	breast:
3	chr12:46345408..46347235-chr12:46357374..46359996,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10161306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1062905	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880867	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10880873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880883	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11183208	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11183210	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs11183211	0.88[CEU][hapmap]
rs11183217	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.82[EUR][1000 genomes]
rs11183219	0.88[CEU][hapmap]
rs11183223	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11183226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11183228	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11183229	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11183234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11183243	0.80[JPT][hapmap]
rs11183251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11183272	0.86[JPT][hapmap]
rs11183273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11183275	0.89[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs11574964	0.95[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs12318248	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12370024	0.84[CEU][hapmap]
rs1366024	0.82[JPT][hapmap]
rs1427750	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17096308	0.90[ASN][1000 genomes]
rs17096361	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1896539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2408437	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4144983	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4768098	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4768099	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4768100	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768667	0.89[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4768670	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768672	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4768673	0.91[ASN][1000 genomes]
rs4768674	0.82[ASN][1000 genomes]
rs4768675	0.82[ASN][1000 genomes]
rs56146240	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56176440	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61924070	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67136007	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs735351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832397	chr12:46265990-46453733	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	esv3439887	chr12:46337377-46370366	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46299000-46381000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:46319200-46362800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:46322600-46360200	Weak transcription	Fetal Brain Male	brain
4	chr12:46326600-46360400	Weak transcription	Small Intestine	intestine
5	chr12:46329800-46371000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr12:46338800-46360000	Weak transcription	Brain Hippocampus Middle	brain
7	chr12:46338800-46360000	Weak transcription	Brain Substantia Nigra	brain
8	chr12:46341800-46365600	Weak transcription	K562	blood
9	chr12:46342000-46360400	Weak transcription	Ovary	ovary
10	chr12:46342000-46360800	Weak transcription	Lung	lung
11	chr12:46342000-46362400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:46342000-46362400	Weak transcription	Fetal Muscle Leg	muscle
13	chr12:46342000-46362400	Weak transcription	Pancreas	Pancrea
14	chr12:46342000-46363000	Weak transcription	Fetal Stomach	stomach
15	chr12:46342000-46364000	Weak transcription	Gastric	stomach
16	chr12:46342200-46360200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:46342200-46361000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:46342200-46365200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:46342200-46369000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:46342400-46360200	Weak transcription	Colonic Mucosa	Colon
21	chr12:46342800-46361400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:46342800-46362400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:46343000-46375000	Weak transcription	NHEK	skin
24	chr12:46348600-46366200	Weak transcription	Thymus	Thymus
25	chr12:46349200-46367000	Weak transcription	Fetal Intestine Small	intestine
26	chr12:46352000-46361000	Weak transcription	Left Ventricle	heart
27	chr12:46352000-46363600	Weak transcription	Aorta	Aorta
28	chr12:46352600-46360400	Strong transcription	Dnd41	blood
29	chr12:46353000-46362400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr12:46355600-46367800	Weak transcription	HMEC	breast
31	chr12:46356400-46360000	Weak transcription	Stomach Mucosa	stomach
32	chr12:46356400-46369200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr12:46356600-46374200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:46357000-46361000	Weak transcription	Psoas Muscle	Psoas
35	chr12:46357000-46364000	Weak transcription	Fetal Intestine Large	intestine
36	chr12:46357000-46366000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:46357000-46371000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr12:46357000-46380400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr12:46357200-46367000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr12:46357200-46369000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr12:46357600-46364200	Weak transcription	Hela-S3	cervix
42	chr12:46357600-46365800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr12:46357600-46367000	Weak transcription	HUVEC	blood vessel
44	chr12:46357600-46380000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr12:46357800-46360000	Weak transcription	A549	lung
46	chr12:46357800-46361400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:46357800-46363400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr12:46357800-46364000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr12:46357800-46365200	Weak transcription	Fetal Lung	lung
50	chr12:46357800-46365400	Weak transcription	Rectal Mucosa Donor 29	rectum

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